MIAMI (CBSMiami) – The storm clouds that have been gathering over the University of Miami finally started to open Tuesday when the NCAA delivered its long awaited notice of allegations against the school, spelling out exactly what the collegiate governing body found during a two-year investigation of UM.

The NCAA began investigating Miami after former booster, and convicted felon, Nevin Shapiro alleged a litany of NCAA rules violations including payments to players, lavish gifts, and others.

The most serious charge the NCAA leveled against Miami was a lack of institutional control. This charge is the worst the NCAA can hit a school with and has in the past led to the death penalty or other very serious penalties against a school.

According to CBS4 news partner the Miami Herald, lack of institutional control is defined by the NCAA as “found when the Committee on Infractions determines that major violations occurred and the institution failed to display adequate compliance measures, sufficient monitoring to ensure the compliance measures are followed and swift action upon learning of a violation.”

The most infamous case of lack of institutional control in college football history came at Southern Methodist University during the 1980’s. SMU was paying players and the corruption reached all the way to the governor’s mansion in Texas.

SMU became the first school to ever receive the “death penalty” in NCAA history. The penalty included shutting down the entire football program for a year and then allowing the school to slowly rebuild the team over a multi-year process. SMU has never fully recovered from the crippling penalty.

While no one expects UM to be hit with a penalty that harsh, the lack of institutional control in the NCAA’s notice of allegations does mean the school will most likely be hit with some sort of sanctions.

UM President Donna Shalala is fighting back against the NCAA and in a Tuesday statement, criticized the NCAA’s investigation, the credibility of Nevin Shapiro and essentially dared the NCAA to impose any further penalties on the school.

“We deeply regret any violations, but we have suffered enough,” Shalala said in a statement issued Tuesday. “We trust that the Committee on Infractions will provide the fairness and integrity missing during the investigative process.”

For Shalala, the fight against the NCAA could be a fight for her job as well. If there was a lack of institutional control, the question is how far up the ladder did it reach? It will come down to a question of what did Shalala know, and when, harkening back to Senator Howard Baker.

According to CBS4 news partner the Miami Herald, a source familiar with the investigation said the charges against UM “could have been worse, but they’re still pretty bad.” The source added that “it’s more than a slap on the wrist. It will be upsetting. But there’s nothing shocking in there.”

The University of Miami’s current game plan is to formulate a response to the notice of allegations, which is due in 90 days to the Committee on Infractions. After that, the school will be called to appear before the Committee on Infractions during a typically day-long hearing.

Once the COI hearing is completed, the Committee will then take the next 6-8 weeks to complete its report on the school’s case before issuing sanctions against the school. After that, UM can appeal the sanctions to a Committee on Infractions appeals committee, which is separate from the COI.

Miami will most likely appear before the COI sometime between May and July. Given that timetable, sanctions against the school will most likely be delivered to the school sometime between the beginning and middle of football season this fall.

The Herald compiled a list of all of the coaches involved with the Shapiro case and it includes a who’s-who of former UM coaches including: former basketball head coach Frank Haith, now the coach at Missouri, and his former assistants Jorge Fernandez, Jake Morton (now at Western Kentucky) and Michael Schwartz (Fresno State); former football assistants Clint Hurtt (Louisville), Joe Pannunzio (Alabama), Jeff Stoutland (formerly Alabama but now with the Philadelphia Eagles), Aubrey Hill (most recently at Florida).

Haith has reportedly received his notice of allegations and it reportedly did not include an unethical conduct charge, which could be good news for Haith and Missouri. If Haith is hit with a show-cause penalty, it could force Mizzou to either fire him or accept sanctions against him that could harm recruiting at Missouri.

From Missouri to Miami to the NCAA itself, no one’s hands have been clean throughout the UM investigation. The ugly situation is closer to being resolved, but there’s still a significant amount of charges, accusations, and other ugliness still to get through before UM and the NCAA call this case closed.